def keyPressed(self, event):
key = event.getKeyCode()
n = KeyboardListener.moves.get(key, 0)
if 0 != n:
self.dstack.shiftSlicesBy(n)
event.consume()
elif KEY.VK_R == key:
self.dstack.reset()
event.consume()
elif KEY.VK_M == key:
self.dstack.mirrorSlicesAt(self.imp.getCurrentSlice())
event.consume()
elif KEY.VK_W == key:
if not event.isControlDown(
): # otherwise, left control+W close the window
width = IJ.getNumber("Window width:",
min(7, self.dstack.size()))
if not (IJ.CANCELED == width):
self.dstack.windowAroundSlice(self.imp.getCurrentSlice(),
width)
event.consume()
if event.isConsumed():
# Refresh
self.imp.setStack(self.dstack)
else:
# Run pre-existing key listeners
for l in self.listeners.get(event.getSource(), []):
if not event.isConsumed():
l.keyPressed(event)
def get_images(minimum=0, maximum=None, exact=None):
''' Returns a list of ImagePlus objects or None if it failed.
Passing None as parameter will trigger a dialog to show up to enter the exact number of images.
:param minimum: The minimum number of images to select (default: 0).
:param maximum: The maximum number of images to select (default: None).
:param exact: Set this to get an exact number of images (default: None).
'''
if not (minimum or maximum or exact):
exact = int(IJ.getNumber("How many images do you want to process?", 3))
def check_count(count):
'''Returns True if the count of images is as required.'''
# print count, exact, minimum, maximum
if exact:
if not count == exact:
return False
else:
if minimum:
if count < minimum:
return False
if maximum:
if count > maximum:
return False
return True
# Option 1: The selected image is a stack and has the demanded size.
if check_count(WindowManager.getCurrentImage().getStackSize()):
return stack_to_list_of_imp(WindowManager.getCurrentImage())
# Option 2: The count of open images matches the demanded number.
image_ids = WindowManager.getIDList()
if exact:
if len(image_ids) < exact:
return None
if len(image_ids) == exact:
return [WindowManager.getImage(img_id) for img_id in image_ids]
# Option 3: The user can select the images from a list.
image_titles = [WindowManager.getImage(id).getTitle() for id in image_ids]
img_count = len(image_ids)
if exact:
img_count = exact
elif maximum:
img_count = maximum
image_titles.append('None')
images_selected = dialogs.create_selection_dialog(image_titles,
range(img_count),
'Select images for drift correction'
)
# dialogs.create_selection_dialog() returns None if canceled
if not images_selected:
return None
# This is only true if 'None has been appended to image_titles and the user selected it.
if len(image_ids) in images_selected:
images_selected.remove(len(image_ids))
if not check_count(len(images_selected)):
return None
image_list = [WindowManager.getImage(image_ids[selection]) for selection in images_selected]
return image_list
def __split(self, event) :
sel = self.getSelected()
if len(sel) != 1 :
IJ.showMessage("only one cell should be selected !")
return
else :
cellname = sel[0]
rois = self.__rm.getRoisAsArray()
self.__rm.runCommand("reset")
n = int(IJ.getNumber("slice to split ?", 1))
for i in range(n) :
self.__rm.addRoi(rois[i])
#print self.__path+cellname+"-a.zip"
self.__rm.runCommand("Save", self.__path+cellname+"-a.zip")
self.__rm.runCommand("reset")
for i in range(n, len(rois)) :
self.__rm.addRoi(rois[i])
self.__rm.runCommand("Save", self.__path+cellname+"-b.zip")
self.__rm.runCommand("reset")
root = self.__path.rsplit(os.path.sep, 2)[0]+os.path.sep
if not path.exists(root+"Cells"+os.path.sep) :os.makedirs(root+"Cells"+os.path.sep, mode=0777)
fichiertemp = open(root+"Cells"+os.path.sep+cellname+"-a.cell","w")
fichiertemp.write("NAMECELL="+cellname+"-a\n")
fichiertemp.write("PATHCELL="+root+"Cells"+os.path.sep+cellname+"-a.cell\n")
fichiertemp.write("PATHROIS="+root+"ROIs"+os.path.sep+cellname+"-a.zip\n")
fichiertemp.write("NSLICES="+str(len(rois))+"\n")
fichiertemp.write("SLICEINIT="+str(1)+"\n")
fichiertemp.write("SLICEEND="+str(n)+"\n")
r = random.randrange(5,205,1)
g = random.randrange(10,210,1)
b = random.randrange(30,230,1)
fichiertemp.write("COLOR="+str(r)+";"+str(g)+";"+str(b)+"\n")
fichiertemp.close()
fichiertemp = open(root+"Cells"+os.path.sep+cellname+"-b.cell","w")
fichiertemp.write("NAMECELL="+cellname+"-b\n")
fichiertemp.write("PATHCELL="+root+"Cells"+os.path.sep+cellname+"-b.cell\n")
fichiertemp.write("PATHROIS="+root+"ROIs"+os.path.sep+cellname+"-b.zip\n")
fichiertemp.write("NSLICES="+str(len(rois))+"\n")
fichiertemp.write("SLICEINIT="+str(n+1)+"\n")
fichiertemp.write("SLICEEND="+str(len(rois))+"\n")
r = random.randrange(5,205,1)
g = random.randrange(10,210,1)
b = random.randrange(30,230,1)
fichiertemp.write("COLOR="+str(r)+";"+str(g)+";"+str(b)+"\n")
fichiertemp.close()
def checkLeafNumbers(dir):
maskdir = os.path.join(dir, "mask")
resdir = os.path.join(dir, "res")
with open(os.path.join(dir, "leafnumbers.csv")) as f:
leafnumbers = [tuple(s.rstrip("\n").split(",")) for s in f.readlines()]
for filename, n in leafnumbers:
n = int(n)
ip = IJ.openImage(os.path.join(maskdir, "mask_%s" % filename.decode('utf-8')))
ip.show()
ans = int(IJ.getNumber("Number of Leaf", n))
if ans < n:
with open(os.path.join(resdir, "res_%s.csv" % os.path.splitext(filename)[0].decode("utf-8")), "r") as f:
header, paResults = readPAResults(f)
paResults = sorted(paResults, key=lambda x: x.area, reverse=True)
with codecs.open(os.path.join(resdir, "res_%s.csv" % os.path.splitext(filename)[0].decode("utf-8")), "w", "utf-8") as f:
table = [header]
table += [row.asRow() for row in paResults[:ans]]
f.writelines(table)
ip.close()
import os
from ij import IJ
import glob
from ij.plugin.frame import RoiManager
_threshold_percent = 0.9
_n_channels = IJ.getNumber("Enter the number of channels used in this experiment (including brightfield)", 3)
def get_percentile(imp, percentile):
IJ.log("Segmenting brightfield with percentile threshold {}".format(percentile))
stats = imp.getRawStatistics()
hist = stats.histogram()
hist_x_min = stats.histMin
hist_x_max = stats.histMax
hist_x_range = hist_x_max - hist_x_min
hist_x_values = []
for bin in range(0, stats.nBins):
#print("Fraction pixels with intensity in bins 0 to {}".format(bin))
integral = sum(hist[0:bin])/sum(hist)
#print(integral)
intensity = hist_x_range * bin/stats.nBins
hist_x_values.append(intensity)
#print(intensity)
def run():
image = IJ.getImage()
minArea = IJ.getNumber("Enter area cutoff: " , 1)
particleRemover(image, minArea)
from ij.measure import CurveFitter
# Utils is a set of utilites for opening images, creating the output directory, saving images closing all windows
# If it is in the Fiji jars/Lib directory, it will be found. Otherwise, an explicit absolute path must be appended to the search path.
# The path in the next line must be changed to appropriate to the system on which this code runs
sys.path.append(os.path.abspath("/home/amw/git/jythonIJdev/libs"))
from Utils import *
close_non_image_windows()
close_image_windows()
# If number of exposures is less than 1, assume default exposure list.
exposures = []
while True:
exposures.append(IJ.getNumber("exposure (ms)", -1))
if exposures[-1] < 0:
exposures.pop()
exposures.sort()
break
if len(exposures) < 2:
exposures = [4, 10, 20, 50, 100, 200, 500, 1000, 2000,
5000] # default exposures that I happen to use
pprint(exposures)
inputImp, inputPrefix, inputDirPath = open_image()
print("image directory path: ", inputDirPath.encode("ascii"))
inputImp.setTitle(inputPrefix)
inputTitle = inputImp.getTitle()
print("image name: ", inputTitle.encode("ascii"))
from ij import IJ
imp = IJ.getImage()
title = imp.getTitle()
title = title[:-4]
interval_units = IJ.getString("Collection interval units: ", 'hrs')
start_time = IJ.getString("Start time: ", '0')
interval_by_units = IJ.getNumber("Collection interval in {}:".format(interval_units), 0.17)
fontsize = IJ.getNumber("Fontsize:", 14)
#get the directory containing the active image
path = IJ.getDirectory("image")
# If the active image is a duplicate of another image open, its path will be False and
# will print as 'None'. If this is the case, have the user choose a directory to put the
# timestamped tif
if not path:
IJ.log("Image has no source directory")
path = IJ.getDirectory("Choose the directory to save the timestamped tif")
else:
pass
height = imp.getHeight()
width = imp.getWidth()
size = imp.getImageStackSize()
IJ.log("Image title: {}".format(title))
IJ.log("Save path: {}".format(path))
IJ.log("Height: {}".format(height))
IJ.log("Width: {}".format(width))
IJ.log("Size: {}".format(size))
